Tug-of-War in a Double-Nanopore System

Abstract

We simulate a tug-of-war (TOW) scenario for a model double-stranded DNA threading through a double nanopore (DNP) system. The DNA, simultaneously captured at both pores is subject to two equal and opposite forces $-{\vec{f}}_L={\vec{f}}_R$ (TOW), where ${\vec{f}}_L$ and ${\vec{f}}_R$ are the forces applied to the left and the right pore respectively. Even though the net force on the DNA polymer $\Delta {\vec{f}}_{LR}={\vec{f}}_L+{\vec{f}}_R=0$, the mean first passage time (MFPT) $⟨\tau ⟩$ depends on the magnitude of the TOW forces $\left|f_L\right|=\left|f_R\right|=f_{LR}$. We qualitatively explain this dependence of $⟨\tau ⟩$ on $f_{LR}$ from the known results for the single-pore translocation of a triblock copolymer. We demonstrate that the time of flight (TOF) of a monomer with index $m$ ($⟨{\tau }_{LR}(m)⟩$) from one pore to the other exhibits quasi-periodic structure commensurate with the distance between the pores $d_{LR}$. Finally, we study the case $\Delta {\vec{f}}_{LR}={\vec{f}}_L+{\vec{f}}_R\ne 0$, and qualitatively reproduce the experimental result of the dependence of the MFPT on $\Delta {\vec{f}}_{LR}$. For a moderate bias, the MFPT for the DNP system for a chain length $N$ follows the same scaling ansatz as that of for the single nanopore, $⟨\tau ⟩=\left(A{N}^{1+\nu }+{\eta }_{pore}N\right){\left(\Delta f_{LR}\right)}^{-1}$, where ${\eta }_{pore}$ is the pore friction, which enables us to estimate $⟨\tau ⟩$ for a long chain. Our Brownian dynamics simulation studies provide fundamental insights and valuable information about the details of the translocation speed obtained from $⟨{\tau }_{LR}(m)⟩$, and accuracy of the translation of the data obtained in the time-domain to units of genomic distances.

8 Pages, 7 figures

References in corpus (6)

• Nonequilibrium dynamics of polymer translocation and straightening
• Influence of polymer-pore interactions on translocation
• Sequence dependence of DNA translocation through a nanopore
• Dynamical Scaling Exponents for Polymer Translocation through a Nanopore
• Comment on ``Passage Times for Unbiased Polymer Translocation through a Narrow Pore''
• Anomalous Polymer Dynamics Is Non-Markovian: Memory Effects and The Generalized Langevin Equation Formulation

Cited by in corpus (2)

• Polymer translocation through nanopore assisted by an environment of active rods
• An efficient Kinetic Monte Carlo to study analyte capture by a nanopore: Transients, boundary conditions and time-dependent fields